Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3215
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 28995
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:7877 original size:44 final size:44
Alignment explanation
Indices: 7828--7966 Score: 122
Period size: 44 Copynumber: 3.2 Consensus size: 44
7818 AGTTACAGAT
7828 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAAC
* * * ** * * * * *
7872 CTTGCC-TCTTTCGGTTGTGATG-G-AGCTGGTTGAAGACAAAAGAT
1 CTTGCCTTCCTGC-ATTGACA-GCGAAGCAGATCGAAGACACAA-AC
* *
7916 CTTGCTTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAAC
7960 CTTGCCT
1 CTTGCCT
7967 CTTTCGGTTG
Statistics
Matches: 66, Mismatches: 23, Indels: 12
0.65 0.23 0.12
Matches are distributed among these distances:
43 19 0.29
44 29 0.44
45 18 0.27
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.25
Consensus pattern (44 bp):
CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAAC
Found at i:7909 original size:43 final size:43
Alignment explanation
Indices: 7860--7997 Score: 129
Period size: 43 Copynumber: 3.2 Consensus size: 43
7850 GAAGCAGATC
7860 GAAGACACAAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTT
1 GAAGACACAAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTT
* * ** * * * *
7903 GAAGACAAAAGATCTTG-CT-TTTCTGCAT-TGACAGCGAAGCAGATC
1 GAAGACACAA-ACCTTGCCTCTTTC-GGTTGTGA-TG-G-AGCTGGTT
*
7948 GAAGACACAAACCTTGCCTCTTTCGGTTGTGATAGAGCTGGTT
1 GAAGACACAAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTT
7991 GAAGACA
1 GAAGACA
7998 AAGGATCTTG
Statistics
Matches: 70, Mismatches: 17, Indels: 16
0.68 0.17 0.16
Matches are distributed among these distances:
42 7 0.10
43 26 0.37
44 12 0.17
45 18 0.26
46 7 0.10
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (43 bp):
GAAGACACAAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTT
Found at i:8166 original size:86 final size:89
Alignment explanation
Indices: 7824--8163 Score: 387
Period size: 88 Copynumber: 3.9 Consensus size: 89
7814 ATGAAGTTAC
* * **
7824 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAGAAACAAACCTTGCCTCCATCGGTTG
*
7889 TGATGGAGCTGGTTGAAGACAAA-
66 TCATGGAGCTGGTTGAAGACAAAG
* * * * **
7912 AGATCTTGCTTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAGAAACAAACCTTGCCTCCATCGGTTG
* *
7977 TGATAGAGCTGGTTGAAGACAAAG
66 TCATGGAGCTGGTTGAAGACAAAG
* * * *
8001 -GATCTTGCCTTCCTACATTAACAGCGAAGCAGATCG-A-AAACAAAGCTTTGCGTCCATCGATT
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAGAAACAAA-CCTTGCCTCCATCGGTT
*
8063 G-CAGTGGAGCTAGTT-AA-A-AAAG
65 GTCA-TGGAGCTGGTTGAAGACAAAG
*
8085 CAGATCTTGCCTTCCTGCATTAACAGCAAAGCAGATC-AA-AAACAAAGCCTTGCCTCCATCGGT
1 -AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAGAAACAAA-CCTTGCCTCCATCGGT
8148 TG-CATTGGAGCTGGTT
64 TGTCA-TGGAGCTGGTT
8164 AAAGGTTACA
Statistics
Matches: 223, Mismatches: 23, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
84 4 0.02
85 1 0.00
86 78 0.35
87 23 0.10
88 117 0.52
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (89 bp):
AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAGAAACAAACCTTGCCTCCATCGGTTG
TCATGGAGCTGGTTGAAGACAAAG
Found at i:8400 original size:44 final size:42
Alignment explanation
Indices: 8351--8674 Score: 196
Period size: 44 Copynumber: 7.6 Consensus size: 42
8341 CCAGAGATCT
*
8351 TATCTCCCTGAGATTACAGCGGAGCAGATCAAGGATAGTAATCC
1 TATCTCCCTGAGATTACAGTGGAGCAGATCAA-GATAGT-ATCC
* * * * * **
8395 TATCTCCTTGAGATTACAATGGAGCGGAT-TA-A-AGGATTT
1 TATCTCCCTGAGATTACAGTGGAGCAGATCAAGATAGTATCC
* * * * * *
8434 TATCTCTCTGA-AGTTACAGTAGAGAAGATCACG-TCAG-GTCT
1 TATCTCCCTGAGA-TTACAGTGGAGCAGATCAAGAT-AGTATCC
* * * *
8475 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTAGAGATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGATC-AAG-A-TAG-TATCC
* * *
8521 TATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCC
1 TATCTCCCTGAGATTACAGTGGAGCAGATC-AAGATAGTATCC
* * * * *
8564 TATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAATAAGAGATCT
1 TATCTCCCTGAGA-TTACAGTGGAGCAGATCAAGAT-AG-TATCC
* * *
8608 TATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCC
1 TATCTCCCTGAGATTACAGTGGAGCAGATC-AAGATAGTATCC
*
8651 TATCTCCCCGA-AGTTACAGTGGAG
1 TATCTCCCTGAGA-TTACAGTGGAG
8675 TGGATTAAAG
Statistics
Matches: 211, Mismatches: 51, Indels: 37
0.71 0.17 0.12
Matches are distributed among these distances:
38 1 0.00
39 23 0.11
40 2 0.01
41 26 0.12
42 10 0.05
43 53 0.25
44 57 0.27
45 6 0.03
46 33 0.16
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.25
Consensus pattern (42 bp):
TATCTCCCTGAGATTACAGTGGAGCAGATCAAGATAGTATCC
Found at i:8539 original size:46 final size:45
Alignment explanation
Indices: 8472--8635 Score: 160
Period size: 46 Copynumber: 3.7 Consensus size: 45
8462 TCACGTCAGG
* *
8472 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTAGAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGA-CAAAGAATTAGAGA
* *
8518 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACT----A
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGA-CAAAGA-ATTAGAGA
* * * ** *
8561 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAA-AATAAGAGA
1 TCTTATCTCCCTGAGA-TTACAGCGGAGCAGACAAAGAATTAGAGA
8605 TCTTATCTCCCTGAGATTACAGCGGAGCAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGA
8636 TCGAAGACAC
Statistics
Matches: 96, Mismatches: 15, Indels: 16
0.76 0.12 0.13
Matches are distributed among these distances:
40 1 0.01
41 1 0.01
42 3 0.03
43 27 0.28
44 27 0.28
45 1 0.01
46 34 0.35
47 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.24
Consensus pattern (45 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGACAAAGAATTAGAGA
Found at i:8669 original size:43 final size:43
Alignment explanation
Indices: 8521--8658 Score: 163
Period size: 43 Copynumber: 3.2 Consensus size: 43
8511 TTAGAGATCT
8521 TATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCC
1 TATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCC
* * * * * ** *
8564 TATCTCCCTGA-AGTTACAGTGGAGCGGAT-TAAAATAAGAGATCT
1 TATCTCCCTGAGA-TTACAGCGGAGCAGATCGAAGA-CA-CTATCC
8608 TATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCC
1 TATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCC
8651 TATCTCCC
1 TATCTCCC
8659 CGAAGTTACA
Statistics
Matches: 74, Mismatches: 16, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
42 4 0.05
43 37 0.50
44 29 0.39
45 4 0.05
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (43 bp):
TATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCC
Found at i:8719 original size:82 final size:85
Alignment explanation
Indices: 8513--8720 Score: 323
Period size: 87 Copynumber: 2.5 Consensus size: 85
8503 CCAAAGAATT
*
8513 AGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGT
1 AGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCCGAAGT
8578 TACAGTGGAGCGGATTAAAATA
66 TACAGTGGAGCGGATT--AATA
8600 AGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCCGAAGT
1 AGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCCGAAGT
*
8665 TACAGTGGAGTGGATT-A-A
66 TACAGTGGAGCGGATTAATA
* * * *
8683 AG-GATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCG
1 AGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCG
8721 CATCAAGTCT
Statistics
Matches: 115, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
82 32 0.28
83 3 0.03
84 1 0.01
87 79 0.69
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (85 bp):
AGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCCGAAGT
TACAGTGGAGCGGATTAATA
Found at i:9484 original size:20 final size:20
Alignment explanation
Indices: 9459--9498 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
9449 CATGACGGAA
9459 GCAGC-AACAGAAACAGAAAC
1 GCAGCAAACAGAAACA-AAAC
*
9479 GCAGCAAACAGTAACAAAAC
1 GCAGCAAACAGAAACAAAAC
9499 AACAATAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.55, C:0.25, G:0.17, T:0.03
Consensus pattern (20 bp):
GCAGCAAACAGAAACAAAAC
Found at i:14341 original size:27 final size:26
Alignment explanation
Indices: 14311--14362 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
14301 AATCGAAATT
*
14311 AAAGTTCAATATATATATTTAGCAATC
1 AAAGTTCAATATATATAATT-GCAATC
**
14338 AAAGTTTTATATATATAATTGCAAT
1 AAAGTTCAATATATATAATTGCAAT
14363 GGATCAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (26 bp):
AAAGTTCAATATATATAATTGCAATC
Found at i:15291 original size:7 final size:7
Alignment explanation
Indices: 15279--15312 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
15269 TGTTGAAATT
15279 GAATTTG
1 GAATTTG
15286 GAATTTG
1 GAATTTG
15293 GAATTTG
1 GAATTTG
15300 GAATTTG
1 GAATTTG
15307 GAATTT
1 GAATTT
15313 TACTTTAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.44
Consensus pattern (7 bp):
GAATTTG
Found at i:16222 original size:13 final size:13
Alignment explanation
Indices: 16204--16229 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16194 TTGTATGTTA
16204 GAATAATTGGTTG
1 GAATAATTGGTTG
16217 GAATAATTGGTTG
1 GAATAATTGGTTG
16230 CATTGTACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (13 bp):
GAATAATTGGTTG
Found at i:20675 original size:3 final size:3
Alignment explanation
Indices: 20657--20725 Score: 54
Period size: 3 Copynumber: 24.0 Consensus size: 3
20647 CATTAAATTA
* * * *
20657 ATT ATT -TT AAT ATT ATT ATT ACT ATT A-T ATT A-C ACT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
20702 ACT ACT ACT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT
20726 TCCTCATTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
2 5 0.09
3 49 0.91
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:20695 original size:13 final size:15
Alignment explanation
Indices: 20667--20717 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
20657 ATTATTTTAA
*
20667 TATTATTATTACTAT
1 TATTATTACTACTAT
20682 TA-TATTAC-ACTAT
1 TATTATTACTACTAT
*
20695 TATTATTACTACTAC
1 TATTATTACTACTAT
20710 TATTATTA
1 TATTATTA
20718 TTATTATTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 7 0.22
14 11 0.34
15 14 0.44
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTATTACTACTAT
Found at i:22973 original size:19 final size:20
Alignment explanation
Indices: 22933--22976 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
22923 GTTTCTTTTG
* *
22933 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
22952 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
22971 GCATTA
1 GCATTA
22977 GACTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:27227 original size:86 final size:85
Alignment explanation
Indices: 27079--27257 Score: 279
Period size: 86 Copynumber: 2.1 Consensus size: 85
27069 ATCAGTAAAA
*
27079 ATCAAAGACAAACCTTGCCTCTCTGTTTGTAGCAGAGCTGGTTGAAGATAGCAAATCTTGCCTTC
1 ATCAAAGACAAACCTTGCCTCTCTGTTTGTAGCAGAGCAGGTTGAAGATAGCAAATCTTGCCTTC
27144 CTGCA-TTGACAGCGAAGCAG
66 CTGCATTTGACAGC-AAGCAG
* * *
27164 ATCGAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCAGGTTGAATATAGCAGATCTTGCCTT
1 ATCAAAGACAAACCTTGCCTCTCT-GTTTGTAGCAGAGCAGGTTGAAGATAGCAAATCTTGCCTT
* *
27229 CCTGTATTTGGCAGCAAGCAG
65 CCTGCATTTGACAGCAAGCAG
27250 ATCAAAGA
1 ATCAAAGA
27258 TGGAAGATTT
Statistics
Matches: 85, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
85 23 0.27
86 55 0.65
87 7 0.08
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.26
Consensus pattern (85 bp):
ATCAAAGACAAACCTTGCCTCTCTGTTTGTAGCAGAGCAGGTTGAAGATAGCAAATCTTGCCTTC
CTGCATTTGACAGCAAGCAG
Found at i:27411 original size:96 final size:94
Alignment explanation
Indices: 27248--27441 Score: 327
Period size: 96 Copynumber: 2.0 Consensus size: 94
27238 GGCAGCAAGC
27248 AGATCAAAGATGGAAGATTTTACCTCCCTGACTACAGTGGAGTACATTAAGCCGATAACTCTATC
1 AGATCAAAGATGGAAGATTTTACCTCCCTGACTACAGTGGAGTACATTAAGCCGATAACTCTATC
27313 TCCCTGCATTTGGCAGTGGAATAGATTGA
66 TCCCTGCATTTGGCAGTGGAATAGATTGA
* *
27342 AGATCAAAGATGGCAGATTTTACCTCCATGTGACTA-AGTGGAGTACATTGAAGCCGATAACTCT
1 AGATCAAAGATGGAAGATTTTACCTCC--CTGACTACAGTGGAGTACATT-AAGCCGATAACTCT
*
27406 ATCTCCCTGTATTTGGCAGTGGAATAGATTGA
63 ATCTCCCTGCATTTGGCAGTGGAATAGATTGA
27438 AGAT
1 AGAT
27442 GCAGATCTTG
Statistics
Matches: 94, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
94 26 0.28
95 13 0.14
96 55 0.59
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (94 bp):
AGATCAAAGATGGAAGATTTTACCTCCCTGACTACAGTGGAGTACATTAAGCCGATAACTCTATC
TCCCTGCATTTGGCAGTGGAATAGATTGA
Found at i:27739 original size:92 final size:93
Alignment explanation
Indices: 27473--27753 Score: 450
Period size: 93 Copynumber: 3.0 Consensus size: 93
27463 TGCGCGAAGC
27473 AGATCAAGATGGCAGA-TTACCTCCCTGACTACAGTAGAGTACATTGAAGCCGATAACTCTATCT
1 AGATCAAGATGGCAGATTTACCTCCCTGACTACAGTAGAGTACATTGAAGCCGATAACTCTATCT
27537 CCCTGTATTTGGCAGTGGAATAGA-TGA
66 CCCTGTATTTGGCAGTGGAATAGATTGA
*
27564 AGATCAAGATGGACAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAA-CCGATAACTCTAT
1 AGATCAAGATGG-CAGA-TTTACCTCCCTGACTACAGTAGAGTACATTGAAGCCGATAACTCTAT
27628 CTCCCTGTATTTGGCAGTGGAATAGATTGA
64 CTCCCTGTATTTGGCAGTGGAATAGATTGA
*
27658 A-ATCGAAGATGGCAGATTTACCTCCATGGACTACAGT-GAGTACATTGAAGCCGAT-ACTCTAT
1 AGATC-AAGATGGCAGATTTACCTCCCT-GACTACAGTAGAGTACATTGAAGCCGATAACTCTA-
27720 TCTCCCTGT-TTTGGCAGTGGAATAGATTGA
63 TCTCCCTGTATTTGGCAGTGGAATAGATTGA
27750 AGAT
1 AGAT
27754 TGCAGATCTT
Statistics
Matches: 179, Mismatches: 2, Indels: 16
0.91 0.01 0.08
Matches are distributed among these distances:
91 12 0.07
92 54 0.30
93 71 0.40
94 42 0.23
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (93 bp):
AGATCAAGATGGCAGATTTACCTCCCTGACTACAGTAGAGTACATTGAAGCCGATAACTCTATCT
CCCTGTATTTGGCAGTGGAATAGATTGA
Found at i:27861 original size:221 final size:221
Alignment explanation
Indices: 27566--27981 Score: 684
Period size: 221 Copynumber: 1.9 Consensus size: 221
27556 ATAGATGAAG
27566 ATCAAGATGGACAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAACCGATAACTCTATCTC
1 ATCAAGATGGACAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAACCGATAACTCTATCTC
*
27631 CCTGTATTTGGCAGTGGAATAGATTGAA-ATCGAAGATGGCAGATTTACCTCCATGGACTACAGT
66 CCTGTATTTGGCAGTGGAATAGATTGAAGATCG-A-AT-GCAGAGTTACCTCCAT-GACTACAGT
*
27695 -GAGTACATTGAAGCCGAT-ACTCTATTCTCCCTGT-TTTGGCAGTGGAATAGATTGAAGATTGC
127 GGAGTACATTGAA-CCGATAACTCTA-TCTCCCTGTATTT-GCAGTGGAATAGATTGAAGATTAC
27757 AGATCTTGCCTTCCTGTATTTGGCAGCGAAGCA
189 AGATCTTGCCTTCCTGTATTTGGCAGCGAAGCA
*
27790 ATCAAGATGG-CAGATTTTACC-CCCTGA-TACAGTGGAGTACATTGAAGCGATAACTCTATCTC
1 ATCAAGATGGACAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAACCGATAACTCTATCTC
*
27852 CCTGTATTTGGCAGTGGAATAGATTGAAGATCGAATGCAGAGTTACCTCCCTGACTACAGTGGAG
66 CCTGTATTTGGCAGTGGAATAGATTGAAGATCGAATGCAGAGTTACCTCCATGACTACAGTGGAG
27917 TACATTGAACCGATAACTCTATCTCCCTGTATTTGCAGTGGAATAGATTGAAGATTACAGATCTT
131 TACATTGAACCGATAACTCTATCTCCCTGTATTTGCAGTGGAATAGATTGAAGATTACAGATCTT
27982 ATCTCCGAAG
Statistics
Matches: 184, Mismatches: 4, Indels: 14
0.91 0.02 0.07
Matches are distributed among these distances:
218 53 0.29
219 35 0.19
220 2 0.01
221 63 0.34
222 10 0.05
223 11 0.06
224 10 0.05
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (221 bp):
ATCAAGATGGACAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAACCGATAACTCTATCTC
CCTGTATTTGGCAGTGGAATAGATTGAAGATCGAATGCAGAGTTACCTCCATGACTACAGTGGAG
TACATTGAACCGATAACTCTATCTCCCTGTATTTGCAGTGGAATAGATTGAAGATTACAGATCTT
GCCTTCCTGTATTTGGCAGCGAAGCA
Found at i:27918 original size:90 final size:87
Alignment explanation
Indices: 27806--27971 Score: 296
Period size: 90 Copynumber: 1.9 Consensus size: 87
27796 ATGGCAGATT
*
27806 TTACCCCCTGATACAGTGGAGTACATTGAAGCGATAACTCTATCTCCCTGTATTTGGCAGTGGAA
1 TTACCCCCTGATACAGTGGAGTACATTGAACCGATAACTCTATCTCCCTGTATTT-GCAGTGGAA
27871 TAGATTGAAGATCGAATGCAGAG
65 TAGATTGAAGATCGAATGCAGAG
27894 TTACCTCCCTGACTACAGTGGAGTACATTGAACCGATAACTCTATCTCCCTGTATTTGCAGTGGA
1 TTACC-CCCTGA-TACAGTGGAGTACATTGAACCGATAACTCTATCTCCCTGTATTTGCAGTGGA
27959 ATAGATTGAAGAT
64 ATAGATTGAAGAT
27972 TACAGATCTT
Statistics
Matches: 75, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
88 5 0.07
89 27 0.36
90 43 0.57
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (87 bp):
TTACCCCCTGATACAGTGGAGTACATTGAACCGATAACTCTATCTCCCTGTATTTGCAGTGGAAT
AGATTGAAGATCGAATGCAGAG
Found at i:28339 original size:43 final size:43
Alignment explanation
Indices: 28290--28466 Score: 121
Period size: 43 Copynumber: 4.1 Consensus size: 43
28280 CTCCCTGATT
28290 ACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTAGGCA
1 ACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTAGGCA
* ** * * ** * *
28333 ACAGTGGAATAGGTCGAAGATTATAGATCTATCTCCCTAAGCA
1 ACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTAGGCA
* * * * * ***
28376 ATAGTGGA-T-CAGGTGAAGAC-GG-CGATTTTACCTCCCT-GATT
1 ACAGTGGAGTACA-TTGAAG-CTGGTAG-TTCTATCTCCCTAGGCA
*
28417 ACAGTGGAGGTACATTGAAGCTGGTAGTTCTATCTCCCTGGGCA
1 ACAGTGGA-GTACATTGAAGCTGGTAGTTCTATCTCCCTAGGCA
28461 ACAGTG
1 ACAGTG
28467 AATAGATCGA
Statistics
Matches: 92, Mismatches: 33, Indels: 17
0.65 0.23 0.12
Matches are distributed among these distances:
41 8 0.09
42 15 0.16
43 59 0.64
44 10 0.11
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (43 bp):
ACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTAGGCA
Found at i:28444 original size:128 final size:128
Alignment explanation
Indices: 27894--28604 Score: 826
Period size: 127 Copynumber: 5.6 Consensus size: 128
27884 GAATGCAGAG
* * * ** * *
27894 TTACCTCCCTGACTACAGTGGAGTACATTGAA-CCGATAACTCTATCTCCCT-GTATTTGCAGTG
1 TTACCTCCCTGATTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTGGCA---ACAGTG
* *
27957 GAATAGATTGAAGATTACAGATCTTATCT-CCGAAGCAATA---GAGCAGGTTGAAGACGG-GTG
63 GAATAGATCGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGG-TGAAGACGGCG-G
28017 ATT
126 ATT
28020 TTACCTCCCTGATTTACAGTGGAGTACATTGAAGC--GTAGTTCTATCTCCCTGGCAACAGTGGA
1 TTACCTCCCTGA-TTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTGGCAACAGTGGA
* * *
28083 ATAGATCGAAGATTACAG-TCTTATCT-CCTAAGCAATAGT-GAGCAGGTCAAGATGGCAGATT
65 ATAGATCGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGGTGAAGACGGCGGATT
* * ** * *
28144 TTACCTCCCTGACTACA-TGGAGTACATTGAAGCTGATAACTCTATCTCCCT-GTATTTGGCAGT
1 TTACCTCCCTGATTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTGGCA----ACAGT
* *
28207 GGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGAAATAGTGGAGCAGGTCGAAGGACGGCG
62 GGAATAGATCGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGGT-GAA-GACGGCG
28272 GATT
125 GATT
28276 TTACCTCCCTGATTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTAGGCAACAGTGGA
1 TTACCTCCCTGATTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCT-GGCAACAGTGGA
* * *
28341 ATAGGTCGAAGATTATAGATC-TATCTCCCTAAGCAATAGTGGATCAGGTGAAGACGGC-GATT
65 ATAGATCGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGGTGAAGACGGCGGATT
28403 TTACCTCCCTGATTACAGTGGAGGTACATTGAAGCTGGTAGTTCTATCTCCCTGGGCAACAGT-G
1 TTACCTCCCTGATTACAGTGGA-GTACATTGAAGCTGGTAGTTCTATCTCCCT-GGCAACAGTGG
28467 AATAGATCGAAGATT-CAGATCTTATC-CCCATAATGCAATAGTGGCAGCAGGTCGAAGACGGGC
64 AATAGATCGAAGATTACAGATCTTATCTCCC-TAA-GCAATAGTGG-AGCAGGT-GAAGAC-GGC
28530 GGATT
124 GGATT
28535 TTA--TCCCTGATTACA---GAGTACATTGAAGTCT-GTAGTTTCTATCTCCCTGGACAACA-TG
1 TTACCTCCCTGATTACAGTGGAGTACATTGAAG-CTGGTAG-TTCTATCTCCCTGG-CAACAGTG
28593 GAATAGATCGAA
63 GAATAGATCGAA
28605 AAAAACAACA
Statistics
Matches: 516, Mismatches: 37, Indels: 63
0.84 0.06 0.10
Matches are distributed among these distances:
122 16 0.03
123 24 0.05
124 60 0.12
125 7 0.01
126 51 0.10
127 126 0.24
128 64 0.12
129 21 0.04
130 52 0.10
131 30 0.06
132 32 0.06
133 31 0.06
135 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (128 bp):
TTACCTCCCTGATTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTGGCAACAGTGGAA
TAGATCGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGGTGAAGACGGCGGATT
Done.